AspS from Chlamydia trachomatis

ABSTRACT

The invention provides aspS polypeptides and DNA (RNA) encoding aspS polypeptides and methods for producing such polypeptides by recombinant techniques. Also provided are methods for utilizing aspS polypeptides to screen for antibacterial compounds.

This application is a divisional of U.S. patent application Ser. No.08/899,244, filed Jul. 23, 1997, now U.S. Pat. No. 5,882,892.

FIELD OF THE INVENTION

This invention relates to newly identified polynucleotides andpolypeptides, and their production and uses, as well as their variants,agonists and antagonists, and their uses. In particular, in these and inother regards, the invention relates to novel polynucleotides andpolypeptides of the aspartyl tRNA synthetase family, hereinafterreferred to as “aspS”.

BACKGROUND OF THE INVENTION

Chlamydiaceae is a family of obligate intracellular parasites. Allmembers share a common developmental cycle. Chlamydia infect a widerange of vertebrate host, particularly humans.

Chlamydia trachomitis is one of the two recognized species of Chlamydia.Human infections caused by C. trachomitis. are widespread. This speciesis one of the most common cause of sexually transmitted disease in theworld. It is also one of the main causes of infertility in humans.

The frequency of Chlamydia trachomatis infections has risen dramaticallyin the past 20 years. This has been attributed to the emergence ofmultiply antibiotic resistant strains and an increasing population ofpeople with weakened immune system. It is no longer uncommon to isolateChlamydia trachomatis strains which are resistant to some or all of thestandard antibiotics. This has created a demand for both newanti-microbial agents and diagnostic tests for this organism.

t-RNA synthetases have a primary role in protein synthesis according tothe following scheme:

Enzyme+ATP+AA Enzyme.AA−AMP+PPi

Enyme.AA−AMP+t-RNA Enzyme+AMP+AA-t-RNA

in which AA is an amino acid.

Inhibition of this process leads to a reduction in the levels of chargedt-RNA and this triggers a cascade of responses known as the stringentresponse, the result of which is the induction of a state of dormancy inthe organism. As such selective inhibitors of bacterial t-RNA synthetasehave potential as antibacterial agents. One example of such is mupirocinwhich is a selective inhibitor of isoleucyl t-RNA synthetase. Othert-RNA synthetases are now being examined as possible anti-bacterialtargets, this process being greatly assisted by the isolation of thesynthetase.

Clearly, there is a need for factors, such as the novel compounds of theinvention, that have a present benefit of being useful to screencompounds for antibiotic activity. Such factors are also useful todetermine their role m pathogenesis of infection, dysfunction anddisease. There is also a need for identification and characteization ofsuch factors and their antagonists and agonists which can play a role inpreventing, ameliorating or correcting infections, dysfunctions ordiseases.

The polypeptides of the invention have amino acid sequence homology to aknown Thermus aquaticus aspartyl tRNA synthetase protein.

SUMMARY OF THE INVENTION

It is an object of the invention to provide polypeptides that have beenidentified as novel aspS polypeptides by homology between the amino acidsequence set out in Table 1 [SEQ ID NO: 2] and a known amino acidsequence or sequences of other proteins such as Thermus aquaticusaspartyl tRNA synthetase protein.

It is a further object of the invention to provide polynucleotides thatencode aspS polypeptides, particularly polynucleotides that encode thepolypeptide herein designated aspS.

In a particularly preferred embodiment of the invention thepolynucleotide comprises a region encoding aspS polypeptides comprisingthe sequence set out in Table 1 [SEQ ID NO: 1] which includes a fulllength gene, or a variant thereof.

In another particularly preferred embodiment of the invention there is anovel aspS protein from Chlamydia trachomatis comprising the amino acidsequence of Table 1 [SEQ ID NO: 2], or a variant thereof.

In accordance with another aspect of the invention there is provided anisolated nucleic acid molecule encoding a mature polypeptide expressibleby the Chiamydia trachomatis D/UW-3/Cx strain.

A further aspect of the invention there are provided isolated nucleicacid molecules encoding aspS, particularly Chlamydia trachomatis aspS,including mRNAs, cDNAs, genomic DNAs. Further embodiments of theinvention include biologically, diagnostically, prophylactically,clinically or therapeutically useful variants thereof, and compositionscomprising the same.

In accordance with another aspect of the invention, there is providedthe use of a polynucleotide of the invention for therapeutic orprophylactic purposes, in particular genetic immunization. Among theparticularly preferred embodiments of the invention are naturallyoccurring allelic variants of aspS and polypeptides encoded thereby.

Another aspect of the invention there are provided novel polypeptides ofChlamydia trachomatis referred to herein as aspS as well asbiologically, diagnostically, prophylactically, clinically ortherapeutically useful variants thereof, and compositions comprising thesame.

Among the particularly preferred embodiments of the invention arevariants of aspS polypeptide encoded by naturally occurring alleles ofthe aspS gene.

In a preferred embodiment of the invention there are provided methodsfor producing the aforementioned aspS polypeptides.

In accordance with yet another aspect of the invention, there areprovided inhibitors to such polypeptides, useful as antibacterialagents, including, for example, antibodies.

In accordance with certain preferred embodiments of the invention, thereare provided products, compositions and methods for assessing aspSexpression, treating disease, for example, classic ocular trachoma,inclusion conjunctivitis, genital trachoma, infant pneumonitis,Lymphogranuloma Venerium, incipient trachoma, keratitis, papillaryhypertrophy, corneal infiltration, vulvovaginitis, ear infection,mucopurulent rhinitis, salpingitis, cervicitis, cervical follicles,prostatitis, proctitis, urethritis, lymphogranule inguinale, climaticbubo, tropical bubo, and esthiomene., assaying genetic variation, andadministering a aspS polypeptide or polynucleotide to an organism toraise an immnunological response against a bacteria, especially aChlamydia trachomatis bacteria.

In accordance with certain preferred embodiments of this and otheraspects of the invention there are provided polynucleotides thathybridize to aspS polynucleotide sequences, particularly under stringentconditions.

In certain preferred embodiments of the invention there are providedantibodies against aspS polypeptides.

In other embodiments of the invention there are provided methods foridentifying compounds which bind to or otherwise interact with andinhibit or activate an activity of a polypeptide or polynucleotide ofthe invention comprising: contacting a polypeptide or polynucleotide ofthe invention with a compound to be screened under conditions to permitbinding to or other interaction between the compound and the polypeptideor polynucleotide to assess the binding to or other interaction with thecompound, such binding or interaction being associated with a secondcomponent capable of providing a detectable signal in response to thebinding or interaction of the polypeptide or polynucleotide with thecompound; and determining whether the compound binds to or otherwiseinteracts with and activates or inhibits an activity of the polypeptideor polynucleotide by detecting the presence or absence of a signalgenerated from the binding or interaction of the compound with thepolypeptide or polynucleotide.

In accordance with yet another aspect of the invention, there areprovided aspS agonists and antagonists, preferably bacteriostatic orbacteriocidal agonists and antagonists.

In a further aspect of the invention there are provided compositionscomprising a aspS polynucleotide or a aspS polypeptide foradministration to a cell or to a multicellular organism.

Various changes and modifications within the spirit and scope of thedisclosed invention will become readily apparent to those skilled in theart from reading the following descriptions and from reading the otherparts of the preset disclosure.

GLOSSARY

The following definitions are provided to facilitate understanding ofcertain terms used frequently herein.

“Host cell” is a cell which has been transformed or transfected, or iscapable of transformation or transfection by an exogenous polynucleotidesequence.

“Identity,” as known in the art is a relationship between two or morepolypeptide sequences or two or more polynucleotide sequences, asdetermined by comparing the sequences. In the art, “identity” also meansthe degree of sequence relatedness between polypeptide or polynucleotidesequences, as the case may be, as determined by the match betweenstrings of such sequences. “Identity” and “similarity” can be readilycalculated by known methods, including but not limited to thosedescribed in (Computational Molecular Biology, Lesk, A. M., ed., OxfordUniversity Press, New York, 1988; Biocomputing: Informatics and GenomeProjects, Smith, D. W., ed., Academic Press, New York, 1993; ComputerAnalysis of Sequence Data, Part I, Griffin, A. M., and Griffin, H. G.,eds., Humana Press, New Jersey, 1994; Sequence Analysis in MolecularBiology, von Heinje, G., Academic Press, 1987; and Sequence AnalysisPrimer, Gribskov, M. and Devereux, J., eds., M Stockton Press, New York,1991; and Carillo, H., and Lipman, D., SLAM J. Applied Math., 48: 1073(1988). Preferred methods to determine identity are designed to give thelargest match between the sequences tested. Methods to determineidentity and similarity are codified in publicly available computerprograms. Preferred computer program methods to determine identity andsimilarity between two sequences include, but are not limited to, theGCG program package (Devereux, J., et al., Nucleic Acids Research 12(1):387 (1984)), BLASTP, BLASIN, and FASTA (Atschul, S. F. et al., J. Molec.Biol. 215: 403-410 (1990). The BLAST X program is publicly availablefrom NCBI and other sources (BLAST Manual, Altschul, S., et al., NCBINLM NIH Bethesda, Md. 20894; Altschul, S., et al., J. Mol. Biol. 215:403-410 (1990). As an illustration, by a polynucleotide having anucleotide sequence having at least, for example, 95% “identity” to areference nucleotide sequence of SEQ ID NO: 1 it is intended that thenucleotide sequence of the polynucleotide is identical to the referencesequence except that the polynucleotide sequence may include up to fivepoint mutations per each 100 nucleotides of the reference nucleotidesequence of SEQ ID NO: 1. In other words, to obtain a polynucleotidehaving a nucleotide sequence at least 95% identical to a referencenucleotide sequence, up to 5% of the nucleotides in the referencesequence may be deleted or substituted with another nucleotide, or anumber of nucleotides up to 5% of the total nucleotides in the referencesequence may be inserted into the reference sequence. These mutations ofthe reference sequence may occur at the 5 or 3 terminal positions of thereference nucleotide sequence or anywhere between those terminalpositions, interspersed either individually among nucleotides in thereference sequence or in one or more contiguous groups within thereference sequence. Analogously , by a polypeptide having an amino acidsequence having at least, for example, 95% identity to a reference aminoacid sequence of SEQ ID NO: 2 is intended that the amino acid sequenceof the polypeptide is identical to the reference sequence except thatthe polypeptide sequence may include up to five amino acid alterationsper each 100 amino acids of the reference amino acid of SEQ ID NO: 2. Inother words, to obtain a polypeptide having an amino acid sequence atleast 95% identical to a reference amino acid sequence, up to 5% of theamino acid residues in the reference sequence may be deleted orsubstituted with another amino acid, or a number of amino acids up to 5%of the total amino acid residues in the reference sequence may beinserted into the reference sequence. These alterations of the referencesequence may occur at the amino or carboxy terminal positions of thereference amino acid sequence or anywhere between those terminalpositions, interspersed either individually among residues in thereference sequence or in one or more contiguous groups within thereference sequence.

“Isolated” means altered “by the hand of man” from its natural state,i.e., if it occurs in nature, it has been changed or removed from itsoriginal environment, or both. For example, a polynucleotide or apolypeptide naturally present in a living organism is not “isolated,”but the same polynucleotide or polypeptide separated from the coexistingmaterials of its natural state is “isolated”, as the term is employedherein.

“Polynucleotide(s)” generally refers to any polynbonucleotide orpolydeoxribonucleotide, which may be unmodified RNA or DNA or modifiedRNA or DNA. “Polynucleotide(s)” include, without limitation, single- anddouble-stranded DNA, DNA that is a mixture of single- anddouble-stranded regions or single-, double- and triple-stranded regions,single- and double-stranded RNA, and RNA that is mixture of single- anddouble-stranded regions, hybrid molecules comprising DNA and RNA thatmay be single-stranded or, more typically, double-stranded, ortriple-stranded regions, or a mixture of single- and double-strandedregions. In addition, “polynucleotide” as used herein refers totriple-stranded regions comprising RNA or DNA or both RNA and DNA. Thestrands in such regions may be from the same molecule or from differentmolecules. The regions may include all of one or more of the molecules,but more typically involve only a region of some of the molecules. Oneof the molecules of a triple-helical region often is an oligonucleotide.As used herein, the term “polynucleotide(s)” also includes DNAs or RNAsas described above that contain one or more modified bases. Thus, DNAsor RNAs with backbones modified for stability or for other reasons are“polynucleotide(s)” as that term is intended herein. Moreover, DNAs orRNAs comprising unusual bases, such as inosine, or modified bases, suchas tritylated bases, to name just two examples, are polynucleotides asthe term is used herein. It will be appreciated that a great variety ofmodifications have been made to DNA and RNA that serve many usefulpurposes known to those of skill in the art. The term“polynucleotide(s)” as it is employed herein embraces such chemically,enzymatically or metabolically modified forms of polynucleotides, aswell as the chemical forms of DNA and RNA characteristic of viruses andcells, including, for example, simple and complex cells.“Polynucleotide(s)” also embraces short polynucleotides often referredto as oligonucleotide(s).

“Polypeptide(s)” refers to any peptide or protein comprising two or moreamino acids joined to each other by peptide bonds or modified peptidebonds. “Polypeptide(s)” refers to both short chains, commonly referredto as peptides, oligopeptides and oligomers and to longer chainsgenerally referred to as proteins. Polypeptides may contain amino acidsother than the 20 gene encoded amino acids. “Polypeptide(s)” includethose modified either by natural processes, such as processing and otherpost-translational modifications, but also by chemical modificationtechniques. Such modifications are well described in basic texts and inmore detailed monographs, as well as in a voluminous researchliterature, and they are well known to those of skill in the art. Itwill be appreciated that the same type of modification may be present inthe same or varying degree at several sites in a given polypeptide.Also, a given polypeptide may contain many types of modifications.Modifications can occur anywhere in a polypeptide, including the peptidebackbone, the amino acid side-chains, and the amino or carboxyl termini.Modifications include, for example, acetylation, acylation,ADP-ribosylation, amidation, covalent attachment of flavin, covalentattachment of a heme moiety, covalent attachment of a nucleotide ornucleotide derivative, covalent attachment of a lipid or lipidderivative, covalent attachment of phosphotidylinositol, cross-linking,cyclization, disulfide bond formation, demethylation, formation ofcovalent cross-links, formation of cysteine, formation of pyroglutamate,formylation, gamma-carboxylation, glycosylation, GPI anchor formation,hydroxylation, iodination, methylation, myristoylaton, oxidation,proteolytic processing, phosphorylation, prenylation, racemization,glycosylation, lipid attachment, sulfation, gamma-carboxylation ofglutamic acid residues, hydroxylation and ADP-ribosylation,selenoylation, sulfation, transfer-RNA mediated addition of amino acidsto proteins, such as arginylation, and ubiquitination. See, forinstance, PROTEINS—STRUCTURE AND MOLECULAR PROPERTIES, 2nd Ed., T. E.Creighton, W. H. Freeman and Company, New York (1993) and Wold, F.,Posttranslational Protein Modifications: Perspectives and Prospects,pgs. 1-12 in POSTTRANSLATIONAL COVALENT MODIFICATION OF PROTEINS, B. C.Johnson, Ed, Academic Press, New York (1983); Seifter et al., MethEnzymol. 182:626-646 (1990) and Rattan et al., Protein Synthesis:Posttranslational Modifications and Aging, Ann. N.Y. Acad. Sci. 663:48-62 (1992). Polypeptides may be branched or cyclic, with or withoutbranching. Cyclic, branched and branched circular polypeptides mayresult from post-translational natural processes and may be made byentirely synthetic methods, as well.

“Variant(s)” as the term is used herein, is a polynucleotide orpolypeptide that differs from a reference polynucleotide or polypeptiderespectively, but retains essential properties. A typical variant of apolynucleotide differs in nucleotide sequence from another, referencepolynucleotide. Changes in the nucleotide sequence of the variant may ormay not alter the amino acid sequence of a polypeptide encoded by thereference polynucleotide. Nucleotide changes may result in amino acidsubstitutions, additions, deletions, fusions and truncations in thepolypeptide encoded by the reference sequence, as discussed below. Atypical variant of a polypeptide differs in amino acid sequence fromanother, reference polypeptide. Generally, differences are limited sothat the sequences of the reference polypeptide and the variant areclosely similar overall and, in many regions, identical. A variant andreference polypeptide may differ in amino acid sequence by one or moresubstitutions, additions, deletions in any combination. A substituted orinserted amino acid residue may or may not be one encoded by the geneticcode. A variant of a polynucleotide or polypeptide may be a naturallyoccurring such as an allelic variant, or it may be a variant that is notknown to occur naturally. Non-naturally occurring variants ofpolynucleotides and polypeptides may be made by mutagenesis techniques,by direct synthesis, and by other recombinant methods known to skilledartisans.

DESCRIPTION OF THE INVENTION

The invention relates to novel aspS polypeptides and polynucleotides asdescribed in greater detail below. In particular, the invention relatesto polypeptides and polynucleotides of a novel aspS of Chlamydiatrachomatis, which is related by amino acid sequence homology to

Thermus aquaticus aspartyl tRNA synthetase polypeptide. The inventionrelates especially to aspS having the nucleotide and amino acidsequences set out in Table 1 [SEQ ID NO: 1] and Table 1 [SEQ ID NO: 2]respectively, and to the aspS nucleotide sequences of the DNA in thestrain and amino acid sequences encoded thereby.

TABLE 1 aspS Polynucleotide and Polypeptide Sequences (A) Sequences fromChlamydia trachomatis aspS polynucleotide sequence [SEQ ID NO:1]. 5′-1ATGAAGTACA GAACGCATAA ATGTAATGAG TTGTCCCTTG ATCATGTGGG 51 GGAACATGTTCGTTTGTCTG GGTGGGTGCA TCGTTACCGT AACCATGGGG 101 GAGTTGTTTT CATTGATTTGCGAGATTGCT TTGGGATTAC TCAGATAGTG 151 TGTCGGCAAG AGGAAAACCC AGAACTTCATCAGCTTATGG ATCAAGTCCG 201 TTCAGAGTGG GTGCTTTGTG TGGAAGGACT TGTTTGTGCTCGGCTAGAGG 251 GGATGGAGAA CCCGAATTTG GTTACAGGTT CTATTGAGGT AGAGGTTTCT301 TCCTTGGAAG TGTTGTCTCG GGCACAGAAT CTTCCTTTTT CCATTTCTGA 351TGAACACATT AATGTAAACG AAGAACTGCG GTTAACTTAT CGCTATTTAG 401 ATATGCGCCGTGGCGATATT TTGGACAGAT TAATGTGCCG ACATAAAGTT 451 ATGTTAGCTT GCAGACAGTATTTGGATGAA CAAGGTTTTA CAGAGGTAGT 501 TACGCCTATC TTAGGAAAAT CTACTCCGGAAGGAGCAAGA GACTACTTAG 551 TCCCTTCCCG TATCTATCCA GGGAATTTTT ATGCTCTTCCACAGTCTCCA 601 CAGTTGTTTA AACAGATTTT GATGGTTGGA GGTTTGGATC GGTATTTCCA651 AATAGCGACC TGTTTCCGTG ATGAAGATTT GCGTGCGGAC CGTCAACCTG 701AGTTTACACA GATCGATATG GAAATGAGCT TTGGTGGGCC AGAGGATCTC 751 TTTCCAGTGGTAGAAGAGCT TGTTGCACGT TTATTTGCTG TGAAAGGGAT 801 TGAATTAAAG GCGCCTTTCCTGAGAATGAC GTATCAAGAA GCTAAAGACT 851 CCTATGGAAC GGACAAACCA GATTTACGTTTCGGCTTGCG CCTCAAAAAT 901 TGTTGTGAAT ATGCACGCAA ATTCACATTC TCGATTTTCTTAGATCAATT 951 AGCTTACGGT GGGACAGTTA AAGGATTTTG TGTTCCGGGC GGAGCAGATA1001 TGTCTAGAAA GCAGTTAGAT ATCTATACAG ATTTCGTTAA GCGCTATGGA 1051GCTATGGGGT TAGTATGGAT TAAAAAACAA GACGGGGGTG TATCGTCTAA 1101 TGTTGCCAAATTCGCTTCGG AAGACGTATT CCAAGAAATG TTTGAAGCTT 1151 TTGAGGCAAA AGACCAAGATATTTTATTGT TAATAGCAGC TCCAGAGGCT 1201 GTTGCTAACC AGGCATTAGA TCATTTGCGTAGGTTGATTG CGAGAGAGCG 1251 TCAACTTTAT GATTCAACGC AATATAATTT TGTATGGATCACGGACTTCC 1301 CGCTTTTTGC TAAAGAGGAA GGCGAGTTAT GTCCAGAGCA TCATCCTTTC1351 ACAGCTCCAT TAGACGAGGA TATCTCGCTT TTAGACTCAG ATCCTTTTGC 1401TGTTCGTTCA TCGAGCTATG ATTTGGTGTT AAATGGTTAT GAAATTGCTT 1451 CTGGTTCTCAGCGTATACAT AATCCAGATT TGCAAAATAA AATATTTGCT 1501 TTATTAAAGC TGTCGCAAGAAAGTGTAAAA GAGAAGTTCG GGTTTTTTAT 1551 TGATGCGTTG AGTTTTGGGA CTCCTCCACATTTAGGGATT GCTCTGGGAT 1601 TAGATCGTAT TATGATGGTT CTAACAGGAG CGGAAACTATTCGAGAAGTG 1651 ATTGCGTTCC CTAAAACACA GAAAGCAGGA GATTTGATGA TGTCGGCACC1701 TTCAGAAATT TTGCCGATTC AATTAAAAGA ACTGGGGTTG AAACTATAA-3′ (B) aspSpolypeptide sequence deduced from the polynucleotide sequence in thistable [SEQ ID NO:2]. NH₂-1 MKYRTHKCNE LSLDHVGEHV RLSGWVHRYR NHGGVVFIDLRDCFGITQIV 51 CRQEENPELH QLMDQVRSEW VLCVEGLVCA RLEGMENPNL VTGSIEVEVS 101SLEVLSRAQN LPFSISDEHI NNNEELRLTY RYLDMRRGDI LDRLMCRHKV 151 MLACRQYLDEQGFTEVVTPI LGKSTPEGAR DYLVPSRIYP GNFYALPQSP 201 QLFKQILMVG GLDRYFQIATCFRDEDLRAD RQPEFTQIDM EMSFGGPEDL 251 FPVVEELVAR LFAVKGIELK APFLRMTYQEAKDSYGTDKP DLRFGLRLKN 301 CCEYARKFTF SIFLDQLAYG GTVKGFCVPG GADMSRKQLDIYTDFVKRYG 351 AMGLVWIKKQ DGGVSSNVAK FASEDVFQEM FEAFEAKDQD ILLLIAAPEA401 VANQALDHLR RLIARERQLY DSTQYNFVWI TDFPLFAKEE GELCPEHHPF 451TAPLDEDISL LDSDPFAVRS SSYDLVLNGY EIASGSQRIH NPDLQNKIFA 501 LLKLSQESVKEKFGFFIDAL SFGTPPHLGI ALGLDRIMMV LTGAETIREV 551 IAFPKTQKAG DLMMSAPSEILPIQLKELGL KL-COOH (C) Polynucleotide sequence embodiments [SEQ IDNO:1]. X—(R₁)_(n)-1 ATGAAGTACA GAACGCATAA ATGTAATGAG TTGTCCCTTGATCATGTGGG 51 GGAACATGTT CGTTTGTCTG GGTGGGTGCA TCGTTACCGT AACCATGGGG 101GAGTTGTTTT CATTGATTTG CGAGATTGCT TTGGGATTAC TCAGATAGTG 151 TGTCGGCAAGAGGAAAACCC AGAACTTCAT CAGCTTATGG ATCAAGTCCG 201 TTCAGAGTGG GTGCTTTGTGTGGAAGGACT TGTTTGTGCT CGGCTAGAGG 251 GGATGGAGAA CCCGAATTTG GTTACAGGTTCTATTGAGGT AGAGGTTTCT 301 TCCTTGGAAG TGTTGTCTCG GGCACAGAAT CTTCCTTTTTCCATTTCTGA 351 TGAACACATT AATGTAAACG AAGAACTGCG GTTAACTTAT CGCTATTTAG401 ATATGCGCCG TGGCGATATT TTGGACAGAT TAATGTGCCG ACATAAAGTT 451ATGTTAGCTT GCAGACAGTA TTTGGATGAA CAAGGTTTTA CAGAGGTAGT 501 TACGCCTATCTTAGGAAAAT CTACTCCGGA AGGAGCAAGA GACTACTTAG 551 TCCCTTCCCG TATCTATCCAGGGAATTTTT ATGCTCTTCC ACAGTCTCCA 601 CAGTTGTTTA AACAGATTTT GATGGTTGGAGGTTTGGATC GGTATTTCCA 651 AATAGCGACC TGTTTCCGTG ATGAAGATTT GCGTGCGGACCGTCAACCTG 701 AGTTTACACA GATCGATATG GAAATGAGCT TTGGTGGGCC AGAGGATCTC751 TTTCCAGTGG TAGAAGAGCT TGTTGCACGT TTATTTGCTG TGAAAGGGAT 801TGAATTAAAG GCGCCTTTCC TGAGAATGAC GTATCAAGAA GCTAAAGACT 851 CCTATGGAACGGACAAACCA GATTTACGTT TCGGCTTGCG CCTCAAAAAT 901 TGTTGTGAAT ATGCACGCAAATTCACATTC TCGATTTTCT TAGATCAATT 951 AGCTTACGGT GGGACAGTTA AAGGATTTTGTGTTCCGGGC GGAGCAGATA 1001 TGTCTAGAAA GCAGTTAGAT ATCTATACAG ATTTCGTTAAGCGCTATGGA 1051 GCTATGGGGT TAGTATGGAT TAAAAAACAA GACGGGGGTG TATCGTCTAA1101 TGTTGCCAAA TTCGCTTCGG AAGACGTATT CCAAGAAATG TTTGAAGCTT 1151TTGAGGCAAA AGACCAAGAT ATTTTATTGT TAATAGCAGC TCCAGAGGCT 1201 GTTGCTAACCAGGCATTAGA TCATTTGCGT AGGTTGATTG CGAGAGAGCG 1251 TCAACTTTAT GATTCAACGCAATATAATTT TGTATGGATC ACGGACTTCC 1301 CGCTTTTTGC TAAAGAGGAA GGCGAGTTATGTCCAGAGCA TCATCCTTTC 1351 ACAGCTCCAT TAGACGAGGA TATCTCGCTT TTAGACTCAGATCCTTTTGC 1401 TGTTCGTTCA TCGAGCTATG ATTTGGTGTT AAATGGTTAT GAAATTGCTT1451 CTGGTTCTCA GCGTATACAT AATCCAGATT TGCAAAATAA AATATTTGCT 1501TTATTAAAGC TGTCGCAAGA AAGTGTAAAA GAGAAGTTCG GGTTTTTTAT 1551 TGATGCGTTGAGTTTTGGGA CTCCTCCACA TTTAGGGATT GCTCTGGGAT 1601 TAGATCGTAT TATGATGGTTCTAACAGGAG CGGAAACTAT TCGAGAAGTG 1651 ATTGCGTTCC CTAAAACACA GAAAGCAGGAGATTTGATGA TGTCGGCACC 1701 TTCAGAAATT TTGCCGATTC AATTAAAAGA ACTGGGGTTGAAACTATAA-(R₂)_(n)-Y (D) Polypeptide sequence embodiments [SEQ ID NO:2].X—(R₁)_(n)-1 MKYRTHKCNE LSLDHVGEHV RLSGWVHRYR NHGGVVFIDL RDCFGITQIV 51CRQEENPELH QLMDQVRSEW VLCVEGLVCA RLEGMENPNL VTGSIEVEVS 101 SLEVLSRAQNLPFSISDEHI NVNEELRLTY RYLDMRRGDI LDRLMCRHKV 151 MLACRQYLDE QGFTEVVTPILGKSTPEGAR DYLVPSRIYP GNFYALPQSP 201 QLFKQILMVG GLDRYFQIAT CFRDEDLRADRQPEFTQIDM EMSFGGPEDL 251 FPVVEELVAR LFAVKGIELK APFLRMTYQE AKDSYGTDKPDLRFGLRLKN 301 CCEYARKFTF SIFLDQLAYG GTVKGFCVPG GADMSRKQLD IYTDFVKRYG351 AMGLVWIKKQ DGGVSSNVAK FASEDVFQEM FEAFEAADQD ILLLIAAPEA 401VANQALDHLR RLIARERQLY DSTQYNFVWI TDFPLFAKEE GELCPEHHPF 451 TAPLDEDISLLDSDPFAVRS SSYDLVLNGY EIASGSQRIH NPDLQNKIFA 501 LLKLSQESVK EKFGFFIDALSFGTPPHLGI ALGLDRIMMV LTGAETIREV 551 IAFPKTQKAG DLMMSAPSEI LPIQLKELGLKL-(R₂)_(n)-Y

Polypeptides

The polypeptides of the invention include the polypeptide of Table 1[SEQ ID NO: 2] (in particular the mature polypeptide) as well aspolypeptides and fragments, particularly those which have the biologicalactivity of aspS, and also those which have at least 70% identity to thepolypeptide of Table 1 [SEQ ID NO: 2] or the relevant portion,preferably at least 80% identity to the polypeptide of Table 1 [SEQ IDNO: 2], and more preferably at least 90% similarity (more preferably atleast 90% identity) to the polypeptide of Table 1 [SEQ ID NO: 2] andstill more preferably at least 95% similarity (still more preferably atleast 95% identity) to the polypeptide of Table 1 [SEQ ID NO: 2] andalso include portions of such polypeptides with such portion of thepolypeptide generally containing at least 30 amino acids and morepreferably at least 50 amino acids.

The invention also includes polypeptides of the formula set forth inTable 1 (D) wherein, at the amino terminus, X is hydrogen, and at thecarboxyl terminus, Y is hydrogen or a metal, R₁ and R₂ is any amino acidresidue, and n is an integer between 1 and 1000. Any stretch of aminoacid residues denoted by either R group, where R is greater than 1, maybe either a heteropolymer or a homopolymer, preferably a heteropolymer.

A fragment is a variant polypeptide having an amino acid sequence thatentirely is the same as part but not all of the amino acid sequence ofthe aforementioned polypeptides. As with aspS polypeptides fragments maybe “free-standing,” or comprised within a larger polypeptide of whichthey form a part or region, most preferably as a single continuousregion, a single larger polypeptide.

Preferred fragments include, for example, truncation polypeptides havinga portion of the amino acid sequence of Table 1 [SEQ ID NO:2], or ofvariants thereof, such as a continuous series of residues that includesthe amino terminus, or a continuous series of residues that includes thecarboxyl terminus. Degradation forms of the polypeptides of theinvention in a host cell, particularly a Chlamydia trachomatis, are alsopreferred. Further preferred are fragments characterized by structuralor functional attributes such as fragments that comprise alpha-helix andalpha-helix forming regions, beta-sheet and beta-sheet-forming regions,turn and turn-forming regions, coil and coil-forming regions,hydrophilic regions, hydrophobic regions, alpha amphipathic regions,beta amphipathic regions, flexible regions, surface-forming regions,substrate binding region, and high antigenic index regions.

Also preferred are biologically active fragments which are thosefragments that mediate activities of aspS, including those with asimilar activity or an improved activity, or with a decreasedundesirable activity. Also included are those fragments that areantigenic or immunogenic in an animal, especially in a human.Particularly preferred are fragments comprising receptors or domains ofenzymes that confer a function essential for viability of Chlamydiatrachomatis or the ability to initiate, or maintain cause disease in anindividual, particularly a human.

Variants that are fragments of the polypeptides of the invention may beemployed for producing the corresponding full-length polypeptide bypeptide synthesis; therefore, these variants may be employed asintermediates for producing the full-length polypeptides of theinvention.

Polynucleotides

Another aspect of the invention relates to isolated polynucleotides,including the full length gene, that encode the aspS polypeptide havingthe deduced amino acid sequence of Table 1 [SEQ ID NO: 2] andpolynucleotides closely related thereto and variants thereof.

Using the information provided herein, such as the polynucleotidesequence set out in Table 1 [SEQ ID NO:1], a polynucleotide of theinvention encoding aspS polypeptide may be obtained using standardcloning and screening methods, such as those for cloning and sequencingchromosomal DNA fragments from bacteria using Chlamydia trachomatisD/UW-3/Cx cells as starting material followed by obtaining a full lengthclone. For example, to obtain a polynucleotide sequence of theinvention, such as the sequence given in Table 1 [SEQ ID NO: 1],typically a library of clones of chromosomal DNA of Chiamydiatrachomatis D/UW-3/Cx in E. coli or some other suitable host is probedwith a radiolabeled oligonucleotide, preferably a 17-mer or longer,derived from a partial sequence. Clones carrying DNA identical to thatof the probe can then be distinguished using stringent conditions. Bysequencing the individual clones thus identified with sequencing primersdesigned from the original sequence it is then possible to extend thesequence in both directions to determine the full gene sequence.Conveniently, such sequencing is performed using denatured doublestranded DNA prepared from a plasmid clone. Suitable techniques aredescribed by Maniatis, T., Fritsch, E. F. and Sambrook et al., MOLECULARCLONING, A LABORATORY MANUNAL, 2nd Ed.; Cold Spring Harbor LaboratoryPress, Cold Spring Harbor, New York (1989). (see in particular ScreeningBy Hybridization 1.90 and Sequencing Denatured Double-Stranded DNATemplates 13.70). Illustrative of the invention, the polynucleotide setout in Table 1 [SEQ ID NO: 1] was discovered in a DNA library derivedfrom Clamydia trachomatis D/UW-3/Cx.

The DNA sequence set out in Table 1 [SEQ ID NO: 1] contains an openreading frame encoding a protein having about the number of amino acidresidues set forth in Table 1 [SEQ ID NO: 2] with a deduced molecularweight that can be calculated using amino acid residue molecular weightvalues well known in the art. The polynucleotide of SEQ ID NO: 1,between nucleotide number 1 through number 1746 encodes the polypeptideof SEQ ID NO: 2. The stop codon begins at nucleotide number 1747 of SEQID NO: 1.

The aspS protein of the invention is structurally related to otherproteins of the aspartyl tRNA synthetase family, as shown by the resultsof sequencing the DNA encoding aspS of the strain of the invention. Theprotein exhibits greatest homology to Therrnus aquaticus aspartyl tRNAsynthetase protein among known proteins. aspS of Table 1 [SEQ ID NO: 2]has about 50% identity over its entire length and about 69% similarityover its entire length with the amino acid sequence of Thermus aquaticusaspartyl tRNA synthetase polypeptide. See, SwissProt Accession No.P36419, and Poterszman et al.; FEBS Lett. 325:183-186 (1993).

The invention provides a polynucleotide sequence identical over itsentire length to the coding sequence in Table 1 [SEQ ID NO: 1]. Alsoprovided by the invention is the coding sequence for the maturepolypeptide or a fragment thereof, by itself as well as the codingsequence for the mature polypeptide or a fragment in reading frame withother coding sequence, such as those encoding a leader or secretorysequence, a pre-, or pro- or prepro- protein sequence. Thepolynucleotide may also contain noncoding sequences, including forexample, but not limited to non-coding 5′ and 3′ sequences, such as thetranscribed, non-translated sequences, termination signals, ribosomebinding sites, sequences that stabilize mRNA, introns, polyadenylationsignals, and additional coding sequence which encode additional aminoacids. For example, a marker sequence that facilitates purification ofthe fused polypeptide can be encoded. In certain embodiments of theinvention, the marker sequence is a hexa-histidine peptide, as providedin the pQE vector (Qiagen, Inc.) and described in Gentz et al., Proc.Natl. Acad Sci., USA 86: 821-824 (1989), or an HA tag (Wilson et al.,Cell 37: 767 (1984). Polynucleotides of the invention also include, butare not limited to, polynucleotides comprising a structural gene and itsnaturally associated sequences that control gene expression.

A preferred embodiment of the invention is the polynucleotide ofcomprising nucleotide 1 to 1746 set forth in SEQ ID NO:1 of Table 1which encodes the aspS polypeptide.

The invention also includes polynucleotides of the formula set forth inTable 1 (C) wherein, at the 5′ end of the molecule, X is hydrogen, andat the 3′ end of the molecule, Y is hydrogen or a metal, R₁ and R₂ isany nucleic acid residue, and n is an integer between 1 and 1000. Anystretch of nucleic acid residues denoted by either R group, where R isgreater tan 1, may be either a heteropolymer or a homopolymer,preferably a heteropolymer.

The term “polynucleotide encoding a polypeptide” as used hereinencompasses polynucleotides that include a sequence encoding apolypeptide of the invention, particularly a bacterial polypeptide andmore particularly a polypeptide of the Chlamydia trachomatis aspS havingthe amino acid sequence set out in Table 1 [SEQ ID NO:2]. The term alsoencompasses polynucleotides that include a single continuous region ordiscontinuous regions encoding the polypeptide (for example, interruptedby integrated phage or an insertion sequence or editing) together withadditional regions, that also may contain coding and/or non-codingsequences.

The invention further relates to variants of the polynucleotidesdescribed herein that encode for variants of the polypeptide having thededuced amino acid sequence of Table 1 [SEQ ID NO: 2]. Variants that arefragments of the polynucleotides of the invention may be used tosynthesize full-length polynucleotides of the invention.

Further particularly preferred embodiments are polynucleotides encodingaspS variants, that have the amino acid sequence of aspS polypeptide ofTable 1 [SEQ ID NO: 2] in which several, a few, 5 to 10, 1 to 5, 1 to 3,2, 1 or no amino acid residues are substituted, deleted or added, in anycombination. Especially preferred among these are silent substitutions,additions and deletions, that do not alter the properties and activitiesof aspS.

Further preferred embodiments of the invention are polynucleotides thatare at least 70% identical over their entire length to a polynucleotideencoding aspS polypeptide having the amino acid sequence set out inTable 1 [SEQ ID NO: 2], and polynucleotides that are complementary tosuch polynucleotides. Alternatively, most highly preferred arepolynucleotides that comprise a region that is at least 80% identicalover its entire length to a polynucleotide encoding aspS polypeptide ofthe strain and polynucleotides complementary thereto. In this regard,polynucleotides at least 90% identical over their entire length to thesame are particularly preferred, and among these particularly preferredpolynucleotides, those with at least 95% are especially preferred.Furthermore, those with at least 97% are highly preferred among thosewith at least 95%, and among these those with at least 98% and at least99% are particularly highly preferred, with at least 99% being the morepreferred.

Preferred embodiments are polynucleotides that encode polypeptides thatretain substantially the same biological function or activity as themature polypeptide encoded by the DNA of Table 1 [SEQ ID NO: 1].

The invention further relates to polynucleotides that hybridize to theherein above-described sequences. In this regard, the inventionespecially relates to polynucleotides that hybridize under stringentconditions to the herein above-described polynucleotides. As hereinused, the terms “stringent conditions” and “stringent hybridizationconditions” mean hybridization will occur only if there is at least 95%and preferably at least 97% identity between the sequences. An exampleof stringent hybridization conditions is overnight incubation at 42° C.in a solution comprising: 50% formamide, 5x SSC (150 mM NaCl, 15 mMtrisodium citrate), 50 mM sodium phosphate (pH 7.6), 5x Denhardt'ssolution, 10% dextran sulfate, and 20 micrograms/ml denatured, shearedsalmon sperm DNA, followed by washing the hybridization support in 0.1xSSC at about 65° C. Hybridization and wash conditions are well known andexemplified in Sambrook, et aL, Molecular Cloning: A Laboratory Manual,Second Edition, Cold Spring Harbor, N.Y., (1989), particularly Chapter11 therein.

The invention also provides a polynucleotide consisting essentially of apolynucleotide sequence obtainable by screening an appropriate librarycontaining the complete gene for a polynucleotide sequence set forth inSEQ ID NO: 1 under stringent hybridization conditions with a probehaving the sequence of said polynucleotide sequence set forth in SEQ IDNO: 1 or a fragment thereof; and isolating said DNA sequence. Fragmentsuseful for obtaining such a polynucleotide include, for example, probesand primers described elsewhere herein.

As discussed additionally herein regarding polynucleotide assays of theinvention, for instance, polynucleotides of the invention as discussedabove, may be used as a hybridization probe for RNA, cDNA and genomicDNA to isolate fill-length cDNAs and genomic clones encoding aspS and toisolate cDNA and genomic clones of other genes that have a high sequencesimilarity to the aspS gene. Such probes generally will comprise atleast 15 bases. Preferably, such probes will have at least 30 bases andmay have at least 50 bases. Particularly preferred probes will have atleast 30 bases and will have 50 bases or less.

For example, the coding region of the aspS gene may be isolated byscreening using the DNA sequence provided in SEQ ID NO: 1 to synthesizean oligonucleotide probe. A labeled oligonucleotide having a sequencecomplementary to that of a gene of the invention is then used to screena library of cDNA, genomic DNA or mRNA to determine which members of thelibrary the probe hybridizes to.

The polynucleotides and polypeptides of the invention may be employed,for example, as research reagents and materials for discovery oftreatments of and diagnostics for disease, particularly human disease,as further discussed herein relating to polynucleotide assays.

Polynucleotides of the invention that are oligonucleotides derived fromthe sequences of SEQ ID NOS: 1 and/or 2 may be used in the processesherein as described, but preferably for PCR, to determine whether or notthe polynucleotides identified herein in whole or in part aretranscribed in bacteria in infected tissue. It is recognized that suchsequences will also have utility in diagnosis of the stage of infectionand type of infection the pathogen has attained.

The invention also provides polynucleotides that may encode apolypeptide that is the mature protein plus additional amino orcarboxyl-terminal amino acids, or amino acids interior to the maturepolypeptide (when the mature form has more than one polypeptide chain,for instance). Such sequences may play a role in processing of a proteinfrom precursor to a mature form, may allow protein transport, maylengthen or shorten protein half-life or may facilitate manipulation ofa protein for assay or production, among other things. As generally isthe case in vivo, the additional amino acids may be processed away fromthe mature protein by cellular enzymes.

A precursor protein, having the mature form of the polypeptide fused toone or more prosequences may be an inactive form of the polypeptide.When prosequences are removed such inactive precursors generally areactivated. Some or all of the prosequences may be removed beforeactivation. Generally, such precursors are called proproteins.

In sum, a polynucleotide of the invention may encode a mature protein, amature protein plus a leader sequence (which may be referred to as apreprotein), a precursor of a mature protein having one or moreprosequences that are not the leader sequences of a preprotein, or apreproprotein, which is a precursor to a proprotein, having a leadersequence and one or more prosequences, which generally are removedduring processing steps that produce active and mature forms of thepolypeptide.

Vectors, host cells, expression

The invention also relates to vectors that comprise a polynucleotide orpolynucleotides of the invention, host cells that are geneticallyengineered with vectors of the invention and the production ofpolypeptides of the invention by recombinant techniques. Cell-freetranslation systems can also be employed to produce such proteins usingRNAs derived from the DNA constructs of the invention.

For recombinant production, host cells can be genetically engineered toincorporate expression systems or portions thereof or polynucleotides ofthe invention. Introduction of a polynucleotide into the host cell canbe effected by methods described in many standard laboratory manuals,such as Davis et al., BASIC METHODS IN MOLECULAR BIOLOGY, (1986) andSambrook et al., MOLECULAR CLONING: A LABORATORY MANUAL, 2nd Ed., ColdSpring Harbor Laboratory Press, Cold Spring Harbor, N.Y. (1989), suchas, calcium phosphate transfection, DEAE-dextran mediated transfection,transvection, microinjection, cationic lipid-mediated transfection,electroporation, transduction, scrape loading, ballistic introductionand infection.

Representative examples of appropriate hosts include bacterial cells,such as streptococci, staphylococci, enterococci E. coli, streptomycesand Bacillus subtilis cells; fungal cells, such as yeast cells andAspergillus cells; insect cells such as Drosophila S2 and Spodoptera Sf9cells; animal cells such as CHO, COS, HeLa, C127, 3T3, BHK, 293 andBowes melanoma cells; and plant cells.

A great variety of expression systems can be used to produce thepolypeptides of the invention. Such vectors include, among others,chromosomal, episomal and virus-derived vectors, e.g., vectors derivedfrom bacterial plasmids, from bacteriophage, from transposons, fromyeast episomes, from insertion elements, from yeast chromosomalelements, from viruses such as baculovireses, papova viruses, such asSV40, vaccinia viruses, adenoviruses, fowl pox viruses, pseudorabiesviruses and retrovirses, and vectors derived from combinations thereof,such as those derived from plasmid and bacteriophage genetic elements,such as cosmids and phagemids. The expression system constructs maycontain control regions that regulate as well as engender expression.Generally, any system or vector suitable to maintain, propagate orexpress polynucleotides and/or to express a polypeptide in a host may beused for expression in this regard. The appropriate DNA sequence may beinserted into the expression system by any of a variety of well-knownand routine techniques, such as, for example, those set forth inSambrook et al, MOLECULAR CLONING, A LABORATORY MANUAL, (supra).

For secretion of the translated protein into the lumen of theendoplasmic reticulum, into the periplasmic space or into theextracellular environment, appropriate secretion signals may beincorporated into the expressed polypeptide. These signals may beendogenous to the polypeptide or they may be heterologous signals.

Polypeptides of the invention can be recovered and purified fromrecombinant cell cultures by well-known methods including ammoniumsulfate or ethanol precipitation, acid extraction, anion or cationexchange chromatography, phosphocellulose chromatography, hydrophobicinteraction chromatography, affinity chromatography, hydroxylapatitechromatography, and lectin chromatography. Most preferably, highperformance liquid chromatography is employed for purification. Wellknown techniques for refolding protein may be employed to regenerateactive conformation when the polypeptide is denatured during isolationand or purification.

Diagnostic Assays

This invention is also related to the use of the aspS polynucleotides ofthe invention for use as diagnostic reagents. Detection of aspS in aeukaryote, particularly a mammal, and especially a human, will provide adiagnostic method for diagnosis of a disease. Eukaryotes (herein also“individual(s)”), particularly mammals, and especially humans, infectedwith an organism comprising the aspS gene may be detected at the nucleicacid level by a variety of techniques.

Nucleic acids for diagnosis may be obtained from an infectedindividual's cells and tissues, such as bone, blood, muscle, cartilage,and skin. Genomic DNA may be used directly for detection or may beamplified enzymatically by using PCR or other amplification techniqueprior to analysis. RNA or cDNA may also be used in the same ways. Usingamplification, characterization of the species and strain of prokaryotepresent in an individual, may be made by an analysis of the genotype ofthe prokaryote gene. Deletions and insertions can be detected by achange in size of the amplified product in comparison to the genotype ofa reference sequence. Point mutations can be identified by hybridizingamplified DNA to labeled aspS polynucleotide sequences. Perfectlymatched sequences can be distinguished from mismatched duplexes by RNasedigestion or by differences in melting temperatures. DNA sequencedifferences may also be detected by alterations in the electrophoreticmobility of the DNA fragments in gels, with or without denaturingagents, or by direct DNA sequencing. See, e.g., Myers et al., Science,230: 1242 (1985). Sequence changes at specific locations also may berevealed by nuclease protection assays, such as RNase and S1 protectionor a chemical cleavage method. See, e.g., Cotton et al., Proc. Natl.Acad Sci., USA, 85: 4397-4401 (1985).

Cells carrying mutations or polymorphisms in the gene of the inventionmay also be detected at the DNA level by a variety of techniques, toallow for serotyping, for example. For example, RT-PCR can be used todetect mutations. It is particularly preferred to used RT-PCR inconjunction with automated detection systems, such as, for example,GeneScan. RNA or cDNA may also be used for the same purpose, PCR orRT-PCR. As an example, PCR primers complementary to a nucleic acidencoding aspS can be used to identify and analyze mutations. Theseprimers may be used for, among other things, amplifying aspS DNAisolated from a sample derived from an individual. The primers may beused to amplify the gene isolated from an infected individual such thatthe gene may then be subject to various techniques for elucidation ofthe DNA sequence. In this way, mutations in the DNA sequence may bedetected and used to diagnose infection and to serotype and/or classifythe infectious agent.

The invention further provides a process for diagnosing, disease,preferably bacterial infections, more preferably infections by Chlamydiatrachomatis, and most preferably classic ocular trachoma, inclusionconjunctivitis, genital trachoma, infant pneumonitis, LymphogranulomaVenerium, incipient trachoma, keratitis, papillary hypertrophy, cornealinfiltration, vulvovagintis, ear infection, mucopurulent rhinitis,salpingitis, cervicitis, cervical follicles, prostatitis, proctitis,urethritis, lymphogranule inguinale, climatic bubo, tropical bubo, andesthiomene, comprising determining from a sample derived from anindividual a increased level of expression of polynucleotide having thesequence of Table 1 [SEQ ID NO: 1]. Increased or decreased expression ofaspS polynucleotide can be measured using any on of the methods wellknown in the art for the quantation of polynucleotides, such as, forexample, amplification, PCR, RT-PCR, RNase protection, Northern blottingand other hybridization methods.

In addition, a diagnostic assay in accordance with the invention fordetecting over-expression of aspS protein compared to normal controltissue samples may be used to detect the presence of an infection, forexample. Assay techniques that can be used to determine levels of a aspSprotein, in a sample derived from a host are well-known to those ofskill in the art. Such assay methods include radioimmunoassays,competitive-binding assays, Western Blot analysis and ELISA assays.

Antibodies

The polypeptides of the invention or variants thereof or cellsexpressing them can be used as an immunogen to produce antibodiesimmununospecific for such polypeptides. “Antibodies” as used hereinincludes monoclonal and polyclonal antibodies, chimeric, single chain,simianized antibodies and humanized antibodies, as well as Fabfragments, including the products of an Fab innmunolglobulin expressionlibrary.

Antibodies generated against the polypeptides of the invention can beobtained by administering the polypeptides or epitope-bearing fragments,analogues or cells to an animal, preferably a nonhuman, using routineprotocols. For preparation of monoclonal antibodies, any technique knownin the art that provides antibodies produced by continuous cell linecultures can be used. Examples include various techniques, such as thosein Kohler, G. and Milstein, C., Nature 256: 495-497 (1975); Kozbor etal., Immunology Today 4: 72 (1983); Cole et al., pg. 77-96 in MONOCLONALANTIBODIES AND CANCER THERAPY, Alan R. Liss, Inc. (1985).

Techniques for the production of single chain antibodies (U.S. Pat. No.4,946,778) can be adapted to produce single chain antibodies topolypeptides of this invention. Also, transgenic mice, or otherorganisms such as other mammals, may be used to express humanizedantibodies.

Alternatively phage display technology may be utilized to selectantibody genes with binding activities towards the polypeptide eitherfrom repertoires of PCR amplified v-genes of lymphocytes from humansscreened for possessing anti-aspS or from naive libraries (McCafferty,J. et al., (1990), Nature 348, 552-554; Marks, J. et al., (1992)Biotechnology 10, 779-783). The affinity of these antibodies can also beimproved by chain shuffling (Clackson, T. et al., (1991) Nature 352,624-628).

If two antigen binding domains are present each domain may be directedagainst a different epitope—termed ‘bispecific’ antibodies.

The above-described antibodies may be employed to isolate or to identifyclones expressing the polypeptides to purify the polypeptides byaffinity chromatography.

Thus, among others, antibodies against aspS- polypeptide may be employedto treat infections, particularly bacterial infections and especiallyclassic ocular trachoma, inclusion conjunctivitis, genital trachoma,infant pneumonitis, Lymphogranuloma Venerium, incipient trachoma,keratitis, papillary hypetrophy, corneal infiltration, vulvovaginitis,ear infection, mucopurulent rhinitis, salpingitis, cervicitis, cervicalfollicles, prostatitis, proctitis, urethritis, lymphogranule inguinale,climatic bubo, tropical bubo, and esthiomene.

Polypeptide variants include antigenically, epitopically orimmunologically equivalent variants that form a particular aspect ofthis invention. The term “antigenically equivalent derivative” as usedherein encompasses a polypeptide or its equivalent which will bespecifically recognized by certain antibodies which, when raised to theprotein or polypeptide according to the invention, interfere with theimmediate physical interaction between pathogen and mammalian host. Theterm “immunologically equivalent derivative” as used herein encompassesa peptide or its equivalent which when used in a suitable formulation toraise antibodies in a vertebrate, the antibodies act to interfere withthe immediate physical interaction between pathogen and mammalian host.

The polypeptide, such as an antigenically or immunologically equivalentderivative or a fusion protein thereof is used as an antigen to immunizea mouse or other animal such as a rat or chicken. The fusion protein mayprovide stability to the polypeptide. The antigen may be associated, forexample by conjugation, with an immunogenic carrier protein for examplebovine serum albumin (BSA) or keyhole limpet haemocyanin (KLH).Alternatively a multiple antigenic peptide comprising multiple copies ofthe protein or polypeptide, or an antigenically or immunologicallyequivalent polypeptide thereof may be sufficiently antigenic to improveimmunogenicity so as to obviate the use of a carrier.

Preferably, the antibody or variant thereof is modified to make it lessimmunogenic in the individual. For example, if the individual is humanthe antibody may most preferably be “humanized”; where thecomplimentarily determining region(s) of the hybridoma-derived antibodyhas been transplanted into a human monoclonal antibody, for example asdescribed in Jones, P. et al. (1986), Nature 321, 522-525 or Tempest etal., (1991) Biotechnology 9, 266-273.

The use of a polynucleotide of the invention in genetic immunizationwill preferably employ a suitable delivery method such as directinjection of plasmid DNA into muscles (Wolff et al., Hum Mol Genet 1992,1:363, Manthorpe et al., Hum. Gene Ther. 1963:4, 419), delivery of DNAcomplexed with specific protein carriers (Wu et al., J Biol Chem. 1989:264,16985), coprecipitation of DNA with calcium phosphate (Benvenisty &Reshef, PNAS USA, 1986:83,9551), encapsulation of DNA in various formsof liposomes (Kaneda et al., Science 1989:243,375), particle bombardment(Tang et al, Nature 1992, 356:152, Eisenbraun et al, DNA Cell Biol 1993,12:791) and in vivo infection using cloned retroviral vectors (Seeger etal., PNAS USA 1984:81,5849).

Antagonists and agonists—assays and molecules

Polypeptides of the invention may also be used to assess the binding ofsmall molecule substrates and ligands in, for example, cells, cell-freepreparations, chemical libraries, and natural product mixtures. Thesesubstrates and ligands may be natural substrates and ligands or may bestructural or functional mimetics. See, eg., Coligan et al, CurrentProtocols in Immunology 1(2): Chapter 5 (1991).

The invention also provides a method of screening compounds to identifythose which enhance (agonist) or block (antagonist) the action of aspSpolypeptides or polynucleotides, particularly those compounds that arebacteriostatic and/or bacteriocidal. The method of screening may involvehigh-throughput techniques. For example, to screen for agonists orantagoists, a synthetic reaction mix, a cellular compartment, such as amembrane, cell envelope or cell wall, or a preparation of any thereof,comprising aspS polypeptide and a labeled substrate or ligand of suchpolypeptide is incubated in the absence or the presence of a candidatemolecule that may be a aspS agonist or antagonist. The ability of thecandidate molecule to agonize or antagonize the aspS polypeptide isreflected in decreased binding of the labeled ligand or decreasedproduction of product from such substrate. Molecules that bindgratuitously, Le., without inducing the effects of aspS polypeptide aremost likely to be good antagonists. Molecules that bind well andincrease the rate of product production from substrate are agonists.Detection of the rate or level of production of product from substratemay be enhanced by using a reporter system. Reporter systems that may beuseful in this regard include but are not limited to colorimetriclabeled substrate converted into product, a reporter gene that isresponsive to changes in aspS polynucleotide or polypeptide activity,and binding assays known in the art.

Another example of an assay for aspS antagonists is a competitive assaythat combines aspS and a potential antagonist with aspS-bindingmolecules, recombinant aspS binding molecules, natural substrates orligands, or substrate or ligand mimetics, under appropriate conditionsfor a competitive inhibition assay. The aspS protein can be labeled,such as by radioactivity or a colorimetric compound, such that thenumber of aspS molecules bound to a binding molecule or converted toproduct can be determined accurately to assess the effectiveness of thepotential antagonist

Potential antagonists include small organic molecules, peptides,polypeptides and antibodies that bind to a polynucleotide or polypeptideof the invention and thereby inhibit or extinguish its activity.Potential antagonists also may be small organic molecules, a peptide, apolypeptide such as a closely related protein or antibody that binds thesame sites on a binding molecule, such as a binding molecule, withoutinducing aspS-induced activities, thereby preventing the action of aspSby excluding aspS from binding.

Potential antagonists include a small molecule that binds to andoccupies the binding site of the polypeptide thereby preventing bindingto cellular binding molecules, such that normal biological activity isprevented. Examples of small molecules include but are not limited tosmall organic molecules, peptides or peptide-like molecules. Otherpotential antagonists include antisense molecules (see Okano, J.Neurochem. 56: 560 (1991); OLIGODEOXYIUCLEOTIDES AS ANTISENSE INHIBITORSOF GENE EXPRESSION, CRC Press, Boca Raton, FLa. (1988), for adescription of these molecules). Preferred potential antagonists includecompounds related to and variants of aspS.

Each of the DNA sequences provided herein may be used in the discoveryand development of antibacterial compounds. The encoded protein, uponexpression, can be used as a target for the screening of antibacterialdrugs. Additionally, the DNA sequences encoding the amino terminalregions of the encoded protein or Shine-Delgarno or other translationfacilitating sequences of the respective mRNA can be used to constructantisense sequences to control the expression of the coding sequence ofinterest.

The invention also provides the use of the polypeptide, polynucleotideor inhibitor of the invention to interfere with the initial physicalinteraction between a pathogen and mammalian host responsible forsequelae of infection. In particular the molecules of the invention maybe used: in the prevention of adhesion of bacteria, in particular grampositive bacteria, to mammalian extracellular matrix proteins onin-dwelling devices or to extracellular matrix proteins in wounds; toblock aspS protein-mediated mammalian cell invasion by, for example,initiating phosphorylation of mammalian tyrosine kinases (Rosenshine etal., Infect. Immun. 60:2211 (1992); to block bacterial adhesion betweenmammalian extracellular matrix proteins and bacterial aspS proteins thatmediate tissue damage and; to block the normal progression ofpathogenesis in infections initiated other than by the implantation ofin-dwelling devices or by other surgical techniques.

The antagonists and agonists of the invention may be employed, forinstance, to inhibit and treat classic ocular trachoma, inclusionconjunctivitis, genital trachoma, infant pneumonitis, LymphogranulomaVenerium, incipient trachoma, keratitis, papillary hypertrophy, cornealinfiltration, vulvovaginitis, ear infection, mucopulent rhinitis,salpingitis, cervicitis, cervical follicles, prostatitis, proctitis,urethritis, lymphogranule inguinale, climatic bubo, tropical bubo, andesthiomene.

Vaccines

Another aspect of the invention relates to a method for inducing animmunological response in an individual, particularly a mammal whichcomprises inoculating the individual with aspS, or a fragment or variantthereof, adequate to produce antibody and/ or T cell immune response toprotect said individual from infection, particularly bacterial infectionand most particularly Chlamydia trachomatis infection. Also provided aremethods whereby such immunological response slows bacterial replication.Yet another aspect of the invention relates to a method of inducingimmunological response in an individual which comprises delivering tosuch individual a nucleic acid vector to direct expression of aspS, or afragment or a variant thereof, for expressing aspS, or a fragment or avariant thereof in vivo in order to induce an immunological response,such as, to produce antibody and/ or T cell immune response, including,for example, cytokine-producing T cells or cytotoxic T cells, to protectsaid individual from disease, whether that disease is alreadyestablished within the individual or not. One way of administering thegene is by accelerating it into the desired cells as a coating onparticles or otherwise.

Such nucleic acid vector may comprise DNA, RNA, a modified nucleic acid,or a DNA/RNA hybrid.

A further aspect of the invention relates to an immunologicalcomposition which, when introduced into an individual capable or havinginduced within it an immunological response, induces an immunologicalresponse in such individual to a aspS or protein coded therefrom,wherein the composition comprises a recombinant aspS or protein codedtherefrom comprising DNA which codes for and expresses an antigen ofsaid aspS or protein coded therefrom. The immunological response may beused therapeutically or prophylactically and may take the form ofantibody immunity or cellular immunity such as that arising from CTL orCD4+T cells.

A aspS polypeptide or a fragment thereof may be fused with co-proteinwhich may not by itself produce antibodies, but is capable ofstabilizing the first protein and producing a fused protein which willhave immunogenic and protective properties. Thus fused recombinantprotein, preferably further comprises an antigenic co-protein, such aslipoprotein D from Hemophilus influenzae, Glutathione-S-transferase(GSI) or beta-galactosidase, relatively large co-proteins whichsolubilize the protein and facilitate production and purificationthereof. Moreover, the co-protein may act as an adjuvant in the sense ofproviding a generalized stimulation of the immune system. The co-proteinmay be attached to either the amino or carboxy terminus of the firstprotein.

Provided by this invention are compositions, particularly vaccinecompositions, and methods comprising the polypeptides or polynucleotidesof the invention and immunostimulatory DNA sequences, such as thosedescribed in Sato, Y. et al. Science 273: 352 (1996).

Also, provided by this invention are methods using the describedpolynucleotide or particular fragments thereof which have been shown toencode non-variable regions of bacterial cell surface proteins in DNAconstructs used in such genetic immunization experiments in animalmodels of infection with Chlamydia trachomatis will be particularlyuseful for identifying protein epitopes able to provoke a prophylacticor therapeutic immune response. It is believed that this approach willallow for the subsequent preparation of monoclonal antibodies ofparticular value from the requisite organ of the animal successfullyresisting or clearing infection for the development of prophylacticagents or therapeutic treatments of bacterial infection, particularlyChlamydia trachomatis infection, in mammals, particularly humans.

The polypeptide may be used as an antigen for vaccination of a host toproduce specific antibodies which protect against invasion of bacteria,for example by blocking adherence of bacteria to damaged tissue.Examples of tissue damage include wounds in skin or connective tissuecaused, e.g., by mechanical, chemical or thermal damage or byimplantation of indwelling devices, or wounds in the mucous membranes,such as the mouth, mammary glands, urethra or vagina.

The invention also includes a vaccine formulation which comprises animmunogenic recombinant protein of the invention together with asuitable carrier. Since the protein may be broken down in the stomach,it is preferably administered parenterally, including, for example,administration that is subcutaneous, intramuscular, intravenous, orintradermal. Formulations suitable for parenteral administration includeaqueous and non-aqueous sterile injection solutions which may containanti-oxidants, buffers, bacteriostats and solutes which render theformulation insotonic with the bodily fluid, preferably the blood, ofthe individual; and aqueous and non-aqueous sterile suspensions whichmay include suspending agents or thickening agents. The formulations maybe presented in unit-dose or multi-dose containers, for example, sealedampules and vials and may be stored in a freeze-dried conditionrequiring only the addition of the sterile liquid carrier immediatelyprior to use. The vaccine formulation may also include adjuvant systemsfor enhancing the immunogenicity of the formulation, such as oil-inwater systems and other systems known in the art. The dosage will dependon the specific activity of the vaccine and can be readily determined byroutine experimentation.

While the invention has been described with reference to certain aspSprotein, it is to be understood that this covers fragments of thenaturally occurring protein and similar proteins with additions,deletions or substitutions which do not substantially affect theimmunogenic properties of the recombinant protein.

Compositions, kits and administration

The invention also relates to compositions comprising the polynucleotideor the polypeptides discussed above or their agonists or antagonists.The polypeptides of the invention may be employed in combination with anon-sterile or sterile carrier or carriers for use with cells, tissuesor organisms, such as a pharmaceutical carrier suitable foradministration to a subject. Such compositions comprise, for instance, amedia additive or a therapeutically effective amount of a polypeptide ofthe invention and a pharmaceutically acceptable carrier or excipient.Such carriers may include, but are not limited to, saline, bufferedsaline, dextrose, water, glycerol, ethanol and combinations thereof. Theformulation should suit the mode of administration. The inventionfurther relates to diagnostic and pharmaceutical packs and kitscomprising one or more containers filled with one or more of theingredients of the aforementioned compositions of the invention.

Polypeptides and other compounds of the invention may be employed aloneor in conjunction with other compounds, such as therapeutic compounds.

The pharmaceutical compositions may be administered in any effective,convenient manner including, for instance, administration by topical,oral, anal, vaginal, intravenous, intraperitoneal, intramuscular,subcutaneous, intnasal or intradermal routes among others.

In therapy or as a prophylactic, the active agent may be administered toan individual as an injectable composition, for example as a sterileaqueous dispersion, preferably isotonic.

Alternatively the composition may be formulated for topical applicationfor example in the form of ointments, creams, lotions, eye ointments,eye drops, ear drops, mouthwash, impregnated dressings and sutures andaerosols, and may contain appropriate conventional additives, including,for example, preservatives, solvents to assist drug penetration, andemollients in ointments and creams. Such topical formulations may alsocontain compatible conventional carriers, for example cream or ointmentbases, and ethanol or oleyl alcohol for lotions. Such carriers mayconstitute from about 1% to about 98% by weight of the formulation; moreusually they will constitute up to about 80% by weight of theformulation.

For administration to mammals, and particularly humans, it is expectedthat the daily dosage level of the active agent will be from 0.01 mg/kgto 10 mg/kg, typically around 1 mg/kg. The physician in any event willdetermine the actual dosage which will be most suitable for anindividual and will vary with the age, weight and response of theparticular individual. The above dosages are exemplary of the averagecase. There can, of course, be individual instances where higher orlower dosage ranges are merited, and such are within the scope of thisinvention.

In-dwelling devices include surgical implants, prosthetic devices andcatheters, i.e., devices that are introduced to the body of anindividual and remain in position for an extended time. Such devicesinclude, for example, artificial joints, heart valves, pacemakers,vascular grafts, vascular catheters, cerebrospinal fluid shunts, urinarycatheters, continuous ambulatory peritoneal dialysis (CAPD) catheters.

The composition of the invention may be administered by injection toachieve a systemic effect against relevant bacteria shortly beforeinsertion of an in-dwelling device. Treatment may be continued aftersurgery during the in-body time of the device. In addition, thecomposition could also be used to broaden perioperative cover for anysurgical technique to prevent bacterial wound infections, especiallyChlamydia trachomatis wound infections.

Many orthopaedic surgeons consider that humans with prosthetic jointsshould be considered for antibiotic prophylaxis before dental treatmentthat could produce a bacteremia. Late deep infection is a seriouscomplication sometimes leading to loss of the prosthetic joint and isaccompanied by significant morbidity and mortality. It may therefore bepossible to extend the use of the active agent as a replacement forprophylactic antibiotics in this situation.

In addition to the therapy described above, the compositions of thisinvention may be used generally as a wound treatment agent to preventadhesion of bacteria to matrix proteins exposed in wound tissue and forprophylactic use in dental treatment as an alternative to, or inconjunction with, antibiotic prophylaxis.

Alternatively, the composition of the invention may be used to bathe anindwelling device immediately before insertion. The active agent willpreferably be present at a concentration of 1 μg/ml to 10 mg/ml forbathing of wounds or indwelling devices.

A vaccine composition is conveniently in injectable form. Conventionaladjuvants may be employed to enhance the immune response. A suitableunit dose for vaccination is 0.5-5 microgram/kg of antigen, and suchdose is preferably administered 1-3 times and with an interval of 1-3weeks. With the indicated dose range, no adverse toxicological effectswill be observed with the compounds of the invention which wouldpreclude their administration to suitable individuals.

Each reference disclosed herein is incorporated by reference herein inits entirety. Any patent application to which this application claimspriority is also incorporated by reference herein in its entirety.

EXAMPLES

The examples below are carried out using standard techniques, which arewell known and routine to those of skill in the art, except whereotherwise described in detail. The examples are illustrative, but do notlimit the invention.

Example 1

Strain selection, Library Production and Sequencing

The polynucleotide having the DNA sequence given in SEQ ID NO: 1 isobtained, for example from a library of clones of chromosomal DNA ofChlamydia trachomatis in E. coli. The sequencing data from two or moreclones containing overlapping Chlamydia trachomatis DNAs is used toconstruct the contiguous DNA sequence in SEQ ID NO: 1. Libraries may beprepared by routine methods, for example:

Methods 1, 2 and 3 below.

Total cellular DNA is isolated from Chlamydia trachomatis D/UW-3/Cxaccording to standard procedures and size-fractionated by either of twomethods.

Method 1

Total cellular DNA is mechanically sheared by passage through a needlein order to size-fractionate according to standard procedures. DNAfragments of up to 11 kbp in size are rendered blunt by treatment withexonuclease and DNA polymerase, and EcoRI linkers added. Fragments areligated into the vector Lambda ZapII that has been cut with EcoRI, thelibrary packaged by standard procedures and E.coli infected with thepackaged library. The library is amplified by standard procedures.

Method 2

Total cellular DNA is partially hydrolyzed with a one or a combinationof restriction enzymes appropriate to generate a series of fragments forcloning into library vectors (e.g., RsaI, PaII, AluI, Bsh1235I), andsuch fragments are size-fractionated according to standard procedures.EcoRI linkers are ligated to the DNA and the fragments then ligated intothe vector Lambda ZapII that have been cut with EcoRI, the librarypackaged by standard procedures, and E. coli infected with the packagedlibrary. The library is amplified by standard procedures.

Method 3

Total cellular DNA is mechanically or enzymatically fragmented tosize-fractionate according to standard procedures. DNA fragments ofabout 1 kbp in size, after preparing their ends using standardprocedures, are ligated into M13 vector using standard procedures. M13is introduced into E. coli host, such as NM522 (available commercially).Clones with inserts are sequenced using standard procedures.

Example 2

aspS Characterization

The enzyme mediated incorporation of radiolabelled amino acid into tRNAis measured by the aminoacylation method which measures amino acid-tRNAas trichloroacetic acid-precipitable radioactivity from radiolabelledamino acid in the presence of tRNA and ATP (Hughes J, Mellows G andSoughton S, 1980, FEBS Letters, 122:322-324). Thus inhibitors ofaspartyl tRNA synthetase is detected by a reduction in thetrichloroacetic acid precipitable radioactivity relative to the control.Alternatively the tRNA synthetase catalysed partial PPi/ATP exchangereaction which measures the formation of radiolabelled ATP from PPi isused to detect aspartyl tRNA synthetase inhibitors (Calender R & Berg P,1966, Biochemistry, 5, 1681-1690).

2 1749 base pairs nucleic acid double linear unknown 1 ATGAAGTACAGAACGCATAA ATGTAATGAG TTGTCCCTTG ATCATGTGGG GGAACATGTT 60 CGTTTGTCTGGGTGGGTGCA TCGTTACCGT AACCATGGGG GAGTTGTTTT CATTGATTTG 120 CGAGATTGCTTTGGGATTAC TCAGATAGTG TGTCGGCAAG AGGAAAACCC AGAACTTCAT 180 CAGCTTATGGATCAAGTCCG TTCAGAGTGG GTGCTTTGTG TGGAAGGACT TGTTTGTGCT 240 CGGCTAGAGGGGATGGAGAA CCCGAATTTG GTTACAGGTT CTATTGAGGT AGAGGTTTCT 300 TCCTTGGAAGTGTTGTCTCG GGCACAGAAT CTTCCTTTTT CCATTTCTGA TGAACACATT 360 AATGTAAACGAAGAACTGCG GTTAACTTAT CGCTATTTAG ATATGCGCCG TGGCGATATT 420 TTGGACAGATTAATGTGCCG ACATAAAGTT ATGTTAGCTT GCAGACAGTA TTTGGATGAA 480 CAAGGTTTTACAGAGGTAGT TACGCCTATC TTAGGAAAAT CTACTCCGGA AGGAGCAAGA 540 GACTACTTAGTCCCTTCCCG TATCTATCCA GGGAATTTTT ATGCTCTTCC ACAGTCTCCA 600 CAGTTGTTTAAACAGATTTT GATGGTTGGA GGTTTGGATC GGTATTTCCA AATAGCGACC 660 TGTTTCCGTGATGAAGATTT GCGTGCGGAC CGTCAACCTG AGTTTACACA GATCGATATG 720 GAAATGAGCTTTGGTGGGCC AGAGGATCTC TTTCCAGTGG TAGAAGAGCT TGTTGCACGT 780 TTATTTGCTGTGAAAGGGAT TGAATTAAAG GCGCCTTTCC TGAGAATGAC GTATCAAGAA 840 GCTAAAGACTCCTATGGAAC GGACAAACCA GATTTACGTT TCGGCTTGCG CCTCAAAAAT 900 TGTTGTGAATATGCACGCAA ATTCACATTC TCGATTTTCT TAGATCAATT AGCTTACGGT 960 GGGACAGTTAAAGGATTTTG TGTTCCGGGC GGAGCAGATA TGTCTAGAAA GCAGTTAGAT 1020 ATCTATACAGATTTCGTTAA GCGCTATGGA GCTATGGGGT TAGTATGGAT TAAAAAACAA 1080 GACGGGGGTGTATCGTCTAA TGTTGCCAAA TTCGCTTCGG AAGACGTATT CCAAGAAATG 1140 TTTGAAGCTTTTGAGGCAAA AGACCAAGAT ATTTTATTGT TAATAGCAGC TCCAGAGGCT 1200 GTTGCTAACCAGGCATTAGA TCATTTGCGT AGGTTGATTG CGAGAGAGCG TCAACTTTAT 1260 GATTCAACGCAATATAATTT TGTATGGATC ACGGACTTCC CGCTTTTTGC TAAAGAGGAA 1320 GGCGAGTTATGTCCAGAGCA TCATCCTTTC ACAGCTCCAT TAGACGAGGA TATCTCGCTT 1380 TTAGACTCAGATCCTTTTGC TGTTCGTTCA TCGAGCTATG ATTTGGTGTT AAATGGTTAT 1440 GAAATTGCTTCTGGTTCTCA GCGTATACAT AATCCAGATT TGCAAAATAA AATATTTGCT 1500 TTATTAAAGCTGTCGCAAGA AAGTGTAAAA GAGAAGTTCG GGTTTTTTAT TGATGCGTTG 1560 AGTTTTGGGACTCCTCCACA TTTAGGGATT GCTCTGGGAT TAGATCGTAT TATGATGGTT 1620 CTAACAGGAGCGGAAACTAT TCGAGAAGTG ATTGCGTTCC CTAAAACACA GAAAGCAGGA 1680 GATTTGATGATGTCGGCACC TTCAGAAATT TTGCCGATTC AATTAAAAGA ACTGGGGTTG 1740 AAACTATAA1749 582 amino acids amino acid single linear unknown 2 Met Lys Tyr ArgThr His Lys Cys Asn Glu Leu Ser Leu Asp His Val 1 5 10 15 Gly Glu HisVal Arg Leu Ser Gly Trp Val His Arg Tyr Arg Asn His 20 25 30 Gly Gly ValVal Phe Ile Asp Leu Arg Asp Cys Phe Gly Ile Thr Gln 35 40 45 Ile Val CysArg Gln Glu Glu Asn Pro Glu Leu His Gln Leu Met Asp 50 55 60 Gln Val ArgSer Glu Trp Val Leu Cys Val Glu Gly Leu Val Cys Ala 65 70 75 80 Arg LeuGlu Gly Met Glu Asn Pro Asn Leu Val Thr Gly Ser Ile Glu 85 90 95 Val GluVal Ser Ser Leu Glu Val Leu Ser Arg Ala Gln Asn Leu Pro 100 105 110 PheSer Ile Ser Asp Glu His Ile Asn Val Asn Glu Glu Leu Arg Leu 115 120 125Thr Tyr Arg Tyr Leu Asp Met Arg Arg Gly Asp Ile Leu Asp Arg Leu 130 135140 Met Cys Arg His Lys Val Met Leu Ala Cys Arg Gln Tyr Leu Asp Glu 145150 155 160 Gln Gly Phe Thr Glu Val Val Thr Pro Ile Leu Gly Lys Ser ThrPro 165 170 175 Glu Gly Ala Arg Asp Tyr Leu Val Pro Ser Arg Ile Tyr ProGly Asn 180 185 190 Phe Tyr Ala Leu Pro Gln Ser Pro Gln Leu Phe Lys GlnIle Leu Met 195 200 205 Val Gly Gly Leu Asp Arg Tyr Phe Gln Ile Ala ThrCys Phe Arg Asp 210 215 220 Glu Asp Leu Arg Ala Asp Arg Gln Pro Glu PheThr Gln Ile Asp Met 225 230 235 240 Glu Met Ser Phe Gly Gly Pro Glu AspLeu Phe Pro Val Val Glu Glu 245 250 255 Leu Val Ala Arg Leu Phe Ala ValLys Gly Ile Glu Leu Lys Ala Pro 260 265 270 Phe Leu Arg Met Thr Tyr GlnGlu Ala Lys Asp Ser Tyr Gly Thr Asp 275 280 285 Lys Pro Asp Leu Arg PheGly Leu Arg Leu Lys Asn Cys Cys Glu Tyr 290 295 300 Ala Arg Lys Phe ThrPhe Ser Ile Phe Leu Asp Gln Leu Ala Tyr Gly 305 310 315 320 Gly Thr ValLys Gly Phe Cys Val Pro Gly Gly Ala Asp Met Ser Arg 325 330 335 Lys GlnLeu Asp Ile Tyr Thr Asp Phe Val Lys Arg Tyr Gly Ala Met 340 345 350 GlyLeu Val Trp Ile Lys Lys Gln Asp Gly Gly Val Ser Ser Asn Val 355 360 365Ala Lys Phe Ala Ser Glu Asp Val Phe Gln Glu Met Phe Glu Ala Phe 370 375380 Glu Ala Lys Asp Gln Asp Ile Leu Leu Leu Ile Ala Ala Pro Glu Ala 385390 395 400 Val Ala Asn Gln Ala Leu Asp His Leu Arg Arg Leu Ile Ala ArgGlu 405 410 415 Arg Gln Leu Tyr Asp Ser Thr Gln Tyr Asn Phe Val Trp IleThr Asp 420 425 430 Phe Pro Leu Phe Ala Lys Glu Glu Gly Glu Leu Cys ProGlu His His 435 440 445 Pro Phe Thr Ala Pro Leu Asp Glu Asp Ile Ser LeuLeu Asp Ser Asp 450 455 460 Pro Phe Ala Val Arg Ser Ser Ser Tyr Asp LeuVal Leu Asn Gly Tyr 465 470 475 480 Glu Ile Ala Ser Gly Ser Gln Arg IleHis Asn Pro Asp Leu Gln Asn 485 490 495 Lys Ile Phe Ala Leu Leu Lys LeuSer Gln Glu Ser Val Lys Glu Lys 500 505 510 Phe Gly Phe Phe Ile Asp AlaLeu Ser Phe Gly Thr Pro Pro His Leu 515 520 525 Gly Ile Ala Leu Gly LeuAsp Arg Ile Met Met Val Leu Thr Gly Ala 530 535 540 Glu Thr Ile Arg GluVal Ile Ala Phe Pro Lys Thr Gln Lys Ala Gly 545 550 555 560 Asp Leu MetMet Ser Ala Pro Ser Glu Ile Leu Pro Ile Gln Leu Lys 565 570 575 Glu LeuGly Leu Lys Leu 580

What is claimed is:
 1. An isolated polypeptide comprising SEQ ID NO: 2.2. A composition comprising the isolated polypeptide of claim 1 and apharmaceutically acceptable carrier.
 3. An isolated fusion polypeptidecomprising a heterologous amino acid sequence fused to SEQ ID NO:
 2. 4.A composition comprising the isolated fusion polypeptide of claim 3 anda pharmaceutically acceptable carrier.
 5. The isolated polypeptide ofclaim 1, wherein the isolated polypeptide consists of SEQ ID NO:
 2. 6. Acomposition comprising the isolated polypeptide of claim 5 and apharmaceutically acceptable carrier.